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Two machines, invented by Giovanni, appeared in Mewtwo Returns. The Team Rocket boss noted that it required a significant investment to create them.
One is red, while the other is gray. They were meant to turn Mewtwo into Giovanni's puppet, each using an energy orb as a weapon. The first time Mewtwo encountered them, it was able to knock them away with its Psychic powers. However, they were not destroyed; instead, the machines created an energy orb that Mewtwo was forced to walk into.
Once inside, Giovanni threatened to destroy all of the cloned Pokémon. However, even though Mewtwo could no longer control its own body, its mind was not truly controlled by Giovanni. Seeing this, Giovanni then realized that Mewtwo's body will be destroyed, but ultimately decided to keep Mewtwo within the orb to determine whose will was stronger.
Ash and his friends arrived and attempted to deactivate the machines. However, even with the help of Pikachu, Meowth, and the clones, they are unable to be destroyed. Mewtwo, using the last of its strength, finally destroyed both machines.